Cruickshank D W
Chemistry Department, UMIST, Manchester M60 1QD, England.
Acta Crystallogr D Biol Crystallogr. 1999 Mar;55(Pt 3):583-601. doi: 10.1107/s0907444998012645.
Full-matrix least squares is taken as the basis for an examination of protein structure precision. A two-atom protein model is used to compare the precisions of unrestrained and restrained refinements. In this model, restrained refinement determines a bond length which is the weighted mean of the unrestrained diffraction-only length and the geometric dictionary length. Data of 0.94 A resolution for the 237-residue protein concanavalin A are used in unrestrained and restrained full-matrix inversions to provide standard uncertainties sigma(r) for positions and sigma(l) for bond lengths. sigma(r) is as small as 0.01 A for atoms with low Debye B values but increases strongly with B. The results emphasize the distinction between unrestrained and restrained refinements and between sigma(r) and sigma(l). Other full-matrix inversions are reported. Such inversions require massive calculations. Several approximate methods are examined and compared critically. These include a Fourier map formula [Cruickshank (1949). Acta Cryst. 2, 65-82], Luzzati plots [Luzzati (1952). Acta Cryst. 5, 802-810] and a new diffraction-component precision index (DPI). The DPI estimate of sigma(r, Bavg) is given by a simple formula. It uses R or Rfree and is based on a very rough approximation to the least-squares method. Many examples show its usefulness as a precision comparator for high- and low-resolution structures. The effect of restraints as resolution varies is examined. More regular use of full-matrix inversion is urged to establish positional precision and hence the precision of non-dictionary distances in both high- and low-resolution structures. Failing this, parameter blocks for representative residues and their neighbours should be inverted to gain a general idea of sigma(r) as a function of B. The whole discussion is subject to some caveats about the effects of disordered regions in the crystal.
全矩阵最小二乘法被用作检验蛋白质结构精度的基础。使用一个双原子蛋白质模型来比较无约束和有约束精修的精度。在这个模型中，有约束精修确定的键长是仅基于衍射的无约束键长和几何字典键长的加权平均值。将分辨率为0.94 Å的237个残基的伴刀豆球蛋白A的数据用于无约束和有约束的全矩阵反演，以提供位置的标准不确定度σ(r)和键长的标准不确定度σ(l)。对于德拜B值较低的原子，σ(r)小至0.01 Å，但会随B值大幅增加。结果强调了无约束和有约束精修之间以及σ(r)和σ(l)之间的区别。还报道了其他全矩阵反演。这种反演需要大量计算。对几种近似方法进行了检验并进行了严格比较。这些方法包括傅里叶图公式[克鲁克香克（1949年）。《晶体学报》2, 65 - 82]、卢扎蒂图[卢扎蒂（1952年）。《晶体学报》5, 802 - 810]以及一种新的衍射分量精度指数（DPI）。σ(r, Bavg)的DPI估计由一个简单公式给出。它使用R或Rfree，并且基于对最小二乘法的非常粗略的近似。许多例子表明它作为高分辨率和低分辨率结构精度比较器的有用性。研究了分辨率变化时有约束的影响。强烈建议更常规地使用全矩阵反演来确定位置精度，从而确定高分辨率和低分辨率结构中非字典距离的精度。如果做不到这一点，应该对代表性残基及其相邻残基的参数块进行反演，以了解σ(r)作为B的函数的大致情况。关于晶体中无序区域的影响，整个讨论存在一些需要注意的事项。
